Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA, Division of Infectious Diseases, Imperial College London, St-Mary's Campus, Norfolk Place, London W2 1PG, UK and Clare Hall Laboratories, London Research Institute, Cancer Research UK, Hertfordshire EN6 3LD, UK.
Nucleic Acids Res. 2014 Apr;42(8):5164-76. doi: 10.1093/nar/gku136. Epub 2014 Feb 11.
Retroviruses favor target-DNA (tDNA) distortion and particular bases at sites of integration, but the mechanism underlying HIV-1 selectivity is unknown. Crystal structures revealed a network of prototype foamy virus (PFV) integrase residues that distort tDNA: Ala188 and Arg329 interact with tDNA bases, while Arg362 contacts the phosphodiester backbone. HIV-1 integrase residues Ser119, Arg231, and Lys258 were identified here as analogs of PFV integrase residues Ala188, Arg329 and Arg362, respectively. Thirteen integrase mutations were analyzed for effects on integrase activity in vitro and during virus infection, yielding a total of 1610 unique HIV-1 integration sites. Purine (R)/pyrimidine (Y) dinucleotide sequence analysis revealed HIV-1 prefers the tDNA signature (0)RYXRY(4), which accordingly favors overlapping flexible dinucleotides at the center of the integration site. Consistent with roles for Arg231 and Lys258 in sequence specific and non-specific binding, respectively, the R231E mutation altered integration site nucleotide preferences while K258E had no effect. S119A and S119T integrase mutations significantly altered base preferences at positions -3 and 7 from the site of viral DNA joining. The S119A preference moreover mimicked wild-type PFV selectivity at these positions. We conclude that HIV-1 IN residue Ser119 and PFV IN residue Ala188 contact analogous tDNA bases to effect virus integration.
逆转录病毒有利于靶 DNA（tDNA）扭曲和整合部位的特定碱基，但 HIV-1 选择性的机制尚不清楚。晶体结构揭示了原型泡沫病毒（PFV）整合酶残基的网络，该网络可扭曲 tDNA：Ala188 和 Arg329 与 tDNA 碱基相互作用，而 Arg362 与磷酸二酯骨架接触。在这里，HIV-1 整合酶残基 Ser119、Arg231 和 Lys258 分别被鉴定为 PFV 整合酶残基 Ala188、Arg329 和 Arg362 的类似物。分析了 13 种整合酶突变对体外和病毒感染过程中整合酶活性的影响，共产生了 1610 个独特的 HIV-1 整合位点。嘌呤（R）/嘧啶（Y）二核苷酸序列分析表明，HIV-1 优先选择 tDNA 特征（0）RYXRY（4），因此有利于整合位点中心重叠的灵活二核苷酸。与 Arg231 和 Lys258 分别在序列特异性和非特异性结合中的作用一致，R231E 突变改变了整合位点核苷酸偏好性，而 K258E 没有影响。S119A 和 S119T 整合酶突变显著改变了病毒 DNA 连接位点上下游 3 位和 7 位的碱基偏好性。此外，S119A 偏好性模拟了野生型 PFV 在这些位置的选择性。我们得出结论，HIV-1 IN 残基 Ser119 和 PFV IN 残基 Ala188 接触类似的 tDNA 碱基以影响病毒整合。
